While the existence of skin-associated bacteria and fungi has been long-documented with culture-based studies, genomic sequencing studies enable identification of fastidious organisms and the simultaneous study of individual species and microbial communities. My laboratory has performed foundational studies of both the skin microbial (bacterial, fungal, viral) communities of healthy volunteer. We have developed marker based studies utilizing 16S rRNA and ITS to study bacteria and fungi, respectively. We have continued these analysis with shotgun metagenomic studies to simultaneously interrogate the bacterial, fungal, viral compositions of human skin. We track both species and strains and explore the full gene encoding potential of the bacterial communities. We are currently engaged in a longitudinal study to explore the stability of the skin microbial communities at the strain level. Our clinical studies have focused on children with moderate to severe atopic dermatitis (eczema), who often progress to develop other atopic disorders, such as allergic rhinitis (hay fever) and asthma. Our objective is to investigate whether microbial diversity might serve as a biomarker to predict a change in disease progression and to direct an individual patients treatment. Our human skin microbiome research is carried out under clinicaltrials.gov NCT00605878; PI: Segre. We analyzed the composition of bacterial communities during AD disease states to identify characteristics associated with AD flares and improvement post-treatment. Disease severity was assessed quantitatively with SCORAD (SCORing AD), a well-validated clinical tool. Our longitudinal study of pediatric AD patients shows a drop in skin microbial diversity and an increase in Staphylococcus aureus with disease flare (Kong et al, Genome Research, 2012). We found that microbial community structures at sites of disease predilection were dramatically different in AD patients compared with controls. Microbial diversity during AD flares was dependent on recent treatment, with even intermittent treatment linked to greater bacterial diversity. In AD, the proportion of Staphylococcus sequences, particularly S. aureus, was greater during disease flares than at baseline or post-treatment and correlated with worsened disease severity. These findings demonstrate that, as compared to culture-based studies, higher resolution examination of microbiota associated with human disease provides novel insights into global shifts of bacteria relevant to disease progression and treatment. We are exploring strains of Staphylococcus associated with disease flare and testing their immunologic response in mouse models. Mechanistically, we are assessing the skin microbiomes role in driving AD with animal models recapitulating the skin disorder. Future microbiome studies will integrate genetics of both host (human) and microbes, realizing that we are superorganisms with trillions of microbes living in and on our bodies and integratinng gene-environment interactions.